BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 03-03-2016, 08:32 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Quantitative analysis of protein僕igand interactions by NMR

Quantitative analysis of protein僕igand interactions by NMR

Publication date: Available online 3 March 2016
Source:Progress in Nuclear Magnetic Resonance Spectroscopy

Author(s): Ayako Furukawa, Tsuyoshi Konuma, Saeko Yanaka, Kenji Sugase

Protein僕igand interactions have been commonly studied through static structures of the protein僕igand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein僕igand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (K D), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R 2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein僕igand interactions in the intermediate- and slow-exchange regimes. Based on R 2 dispersion or ZZ-exchange, methods that can determine the association rate, k on, dissociation rate, k off, and K D have been developed. In these approaches, R 2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R 2 dispersion and ZZ-exchange methods are suitable for the analysis of protein僕igand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used to analyze population-averaged NMR quantities. Essentially, to apply NMR successfully, both the type of experiment and equation to fit the data must be carefully and specifically chosen for the protein僕igand interaction under analysis. In this review, we first explain the exchange regimes and kinetic models of protein僕igand interactions, and then describe the NMR methods that quantitatively analyze these specific interactions.
Graphical abstract








More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP)
Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP) Publication date: Available online 23 March 2015 Source:Journal of Magnetic Resonance</br> Author(s): David S. Snyder , Mihaela Chantova , Saadia Chaudhry</br> NMR spectroscopy is a powerful tool in describing protein structures and protein activity for pharmaceutical and biochemical development. This study describes a method to determine weak binding ligands in biological systems by using hierarchic diffusion coefficient clustering of multidimensional data obtained...
nmrlearner Journal club 0 03-25-2015 10:15 AM
[NMR paper] Quantitative Analysis of STD-NMR Spectra of Reversibly Forming Ligand-Receptor Complexes.
Quantitative Analysis of STD-NMR Spectra of Reversibly Forming Ligand-Receptor Complexes. Related Articles Quantitative Analysis of STD-NMR Spectra of Reversibly Forming Ligand-Receptor Complexes. Top Curr Chem. 2008;273:15-54 Authors: Krishna NR, Jayalakshmi V Abstract We describe our work on the quantitative analysis of STD-NMR spectra of reversibly forming ligand-receptorcomplexes. This analysis is based on the theory of complete relaxation and conformational exchange matrixanalysis of saturation transfer (CORCEMA-ST) effects. As part...
nmrlearner Journal club 0 04-24-2013 09:48 PM
[NMR paper] NMR-based analysis of protein-ligand interactions.
NMR-based analysis of protein-ligand interactions. NMR-based analysis of protein-ligand interactions. Anal Bioanal Chem. 2013 Apr 18; Authors: Cala O, Guilli鑽e F, Krimm I Abstract Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where...
nmrlearner Journal club 0 04-18-2013 10:12 PM
Journal Highlight: Quantitative NMR: An applicable method for quantitative analysis of medicinal plant extracts and herbal products
Journal Highlight: Quantitative NMR: An applicable method for quantitative analysis of medicinal plant extracts and herbal products http://www.spectroscopynow.com/common/images/thumbnails/13abcca009b.jpgA quantitative NMR method has been reported for quantitative analysis of three medicinal plant extracts and their herbal products without the need of authentic standards. Source: Spectroscopynow.com
nmrlearner General 0 02-03-2013 08:49 AM
[NMR paper] Solid-state NMR analysis of ligand--receptor interactions reveals an induced misfit i
Solid-state NMR analysis of ligand--receptor interactions reveals an induced misfit in the binding site of isorhodopsin. Related Articles Solid-state NMR analysis of ligand--receptor interactions reveals an induced misfit in the binding site of isorhodopsin. Biochemistry. 2004 Dec 28;43(51):16011-8 Authors: Creemers AF, Bovee-Geurts PH, DeGrip WJ, Lugtenburg J, de Groot HJ Rhodopsin is the photosensitive protein of the rod photoreceptor in the vertebrate retina and is a paradigm for the superfamily of G-protein-coupled receptors (GPCRs)....
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] Analysis of protein/ligand interactions with NMR diffusion measurements: the importan
Analysis of protein/ligand interactions with NMR diffusion measurements: the importance of eliminating the protein background. Related Articles Analysis of protein/ligand interactions with NMR diffusion measurements: the importance of eliminating the protein background. J Magn Reson. 2002 Apr;155(2):217-25 Authors: Derrick TS, McCord EF, Larive CK Pulsed-field gradient nuclear magnetic resonance (PFG-NMR) is a well-established method for the determination of translational diffusion coefficients. Recently, this method has found applicability in...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Dynamic NMR studies of ligand-receptor interactions: design and analysis of a rapidly
Dynamic NMR studies of ligand-receptor interactions: design and analysis of a rapidly exchanging complex of FKBP-12/FK506 with a 24 kDa calcineurin fragment. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Dynamic NMR studies of ligand-receptor interactions: design and analysis of a rapidly exchanging complex of FKBP-12/FK506 with a 24 kDa calcineurin...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] On the ligand-protein and ligand-flavin interactions in NADPH-adrenodoxin reductase a
On the ligand-protein and ligand-flavin interactions in NADPH-adrenodoxin reductase as studied by 31P- and 13C-NMR. Use of 13C-enriched FAD as a probe. Related Articles On the ligand-protein and ligand-flavin interactions in NADPH-adrenodoxin reductase as studied by 31P- and 13C-NMR. Use of 13C-enriched FAD as a probe. J Biochem. 1991 Jan;109(1):144-9 Authors: Fujii S, Nonaka Y, Okamoto M, Miura R The interaction between 2',5'-ADP and NADPH-adrenodoxin reductase from bovine adrenocortical mitochondria was examined by titrating the enzyme with...
nmrlearner Journal club 0 08-21-2010 11:16 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 04:43 PM.


Map